Nr,GenBank, RefSeq, UniProt 数据库的异同

2018/03/26 22:16
阅读数 68

Nr,GenBank, RefSeq, UniProt 数据库的异同

 

有的文章在做DEG分析时,会把reads比对到RefSeq的转录组上。我也没搞清楚这和直接比对到常规转录组上有什么区别。

文章:Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming

方法:For differential expression analysis, we aligned reads against the refSeq mouse transcriptome using Bowtie version 0.12.7 (Langmead et al., 2009). Expression levels were then  stimated using eXpress (Roberts and Pachter, 2013) (version 1.3.0), with gene-level effective counts and RPKM values derived from the sum of the corresponding values for all isoforms of a gene.

 

refseq 数据库长啥样?

ftp://ftp.ncbi.nlm.nih.gov/refseq/

进到小鼠里:

mRNA_Prot

mRNA_Prot directory
   Contents: organisms-specific RefSeq transcript and protein data

     {org-name}.files.installed: 
         reports the md5checksum and files included in the directory
         For example: /refseq/H_sapiens/mRNA_Prot/human.files.installed

   File Name Conventions:
	File name formats are as follows:
 	     common_name.#.molecule_type.format_type
        Multiple files may be provided for any given molecule and format type and file 
	names include a numerical increment.  Files with the same numerical increment
	are related by content. 

	For example, the files provided for human are named as:
 	      human.#.rna.fna.gz --fasta report for transcript records
 	      human.#.protein.faa.gz --fasta report for protein records
 	      human.#.rna.gbff.gz  --flatfile report for transcript records
 	      human.#.protein.gpff.gz --flatfile report for protein records

  

下载一个rna.fna文件,里面是这样的:

>NM_001013372.2 Mus musculus neural regeneration protein (Nrp), mRNA
CGGTCCAAGGAATTTTTCTGACAAACGCAATAGGCCGACCAGTACTGGAACGCAGTGCGCTTAGCCCCTTTATGGCGGAG
GCTGCCATGTTAAAACGGAATGAATCGAAACCCTGGAGTCGTGACCCCGGAAGAACCTGCCAGAGCCGGAATTTCGAGTT
CTGCTTCCGGGCCAAACTGTTGGCAGCCTCGAGATGGGGAAGATGGCGGCTGCTGTGGCTTCATTAGCCACGCTGGCTGC
AGAGCCCAGAGAGGATGCTTTCCGGAAGCTTTTCCGCTTCTACCGGCAGAGCCGGCCGGGGACAGCGGACCTGGGAGCCG
TCATCGACTTCTCAGAGGCGCACTTGGCTCGGAGCCCGAAGCCCGGCGTGCCCCAGGTAGGAAAGGAGGAGTAGTGTGTG
CCAGCCTAGCGGCCGACTGGGCCACCCGAGACTGGGCCGCCTCCGGGCCGGCTTTGGAGGGAAGCCCCTGCTGGGCCTGT
CCAGTGAGCTGTAATGTCGAGCGATGAGCGACCAGCTGCCTCGCTGTCCCAACGCTCTGGCCACGGCTTGTGCCTTGCCG
CCATTTCCCCCAACCCACGCGGGCCACGGCTTGTGCCCTGCCGCCATTTCCCCCAACCCACGCGACCTTGCTAAAAAAAA
AAAAAGAAAGAAAAGAAAAGAAAGAAAGAAAGAAAAAAATCTGGAAATTGCTTGTACCTCCTTAACTATCTGTTTAATAC
TAATACGATATTTTGTGTAAAGCTCAGAAGAACATCTTCGTGGACGTTAGGGTGGCCTCATAACTTCAGATAAAAGCAGC
CATTTAATAAGTCTCAAACCGTTAATCCGTTGGGCCTGAGACTCGATCGACCCTGTCTTCTCTGAGGCTTTGAAAGTAAA
GGTAAAATTAGCAGGTTTTTTTCCTGAGAATCTAGGAGCCTGGAGAGATAGCTCAGTAATTAAGAGCATTTACCTACTGG
TGTTCCCAAGAACACCAAGTAGATTTGGTTCCTTGCAGCCACGTGGCAGCTCACAGCCTTCTTGTAACTCTTCCGGAGGA
TCAGACACCCTCTCTTGAGCTCCACAGGAGAGCACTCGTAGACATGTAAATAAACTTCTAAGCTAAATCTAAACAATTTA
TGTACCCTCCCTATTTCTTCGTGATGAGAAGAAAGGGGCCAGAGGGTATG
>NR_046233.2 Mus musculus 45S pre-ribosomal RNA (Rn45s), ribosomal RNA
ACTGACACGCTGTCCTTTCCCTATTAACACTAAAGGACACTATAAAGAGACCCTTTCGATTTAAGGCTGTTTTGCTTGTC

  

还是没发现有什么区别!!!

RefSeq转录本是 从gtf得到的转录本的一个子集

  

 

后面会再详细展开~

 

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